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DMol
1 Introduction

WhatIsDMol?
DMolisafirstprinciples(abinitio)quantumchemistrysoftwarepackagethat
performsaccuratetheoreticalcalculationsonawiderangeofcompounds,including
metalclusters,biologicalcompounds,organometallics,andorganiccompounds.
DMolcalculatesvariationalselfconsistentsolutionstothedensityfunctionaltheory
(DFT)equations,expressedinanumericalatomicorbitalbasis.Thesolutionsto
theseequationsprovidethemolecularwavefunctionsandelectrondensities,which
canbeusedtoevaluatetheenergeticsandtheelectronicandmagneticpropertiesof
thesystem.Inaddition,evaluationoftheenergygradientsprovidesaconvenient
methodfordeterminingtheequilibriumgeometryofthesystem.Theseresults
provideareliablepredictivemethodfortheoreticallyexploringthepropertiesof
unknowncompounds,aswellasforexplaining,onamicroscopicscale,theknown
propertiesofexistingcompounds.Therelativelylowcomputationalrequirementsof
themethodallowthestudyoflargermolecularsystemsthanwouldbepossiblewith
otherabinitiomethods.
ThemainDMolprogramsolvesthemolecularDFTequations.Includedinthe
DMolpackageisDAtom,autilitythatgeneratesatomicbasissets.Inaddition,the
dmol_masterinterface(theinputpreparationutilityusedinthestandalonemodeof
DMol)aidsinpreparingandmodifyinginputfilesandincreatingandsubmitting
jobs.
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TypicalusesforDMolinclude:
Calculatingtheelectronicenergyofmolecularorbitalsinachemicalsystem.
Predictingtheequilibriumgeometryofamolecule.
Determiningtheharmonicvibrationalfrequenciesofpolyatomicmolecules.
Calculatingthermodynamicproperties.
CalculatingthemolecularorbitalcoefficientsforeachtermintheHartreeFock
equation.
Calculatingorbitaleigenvaluesandoccupations.
Performingatomicandbondpopulationanalysis.
Calculatingmoleculardipolemoments.
Calculatingopticalabsorptionspectra.
Determiningmolecularpolarizability.
CalculatingESPfittedcharges.
Calculatingelectricfieldgradientsatnuclei.
EvaluatingeffectofsolventviaCOSMOmodel.
Generatingdataforplottingthechargedensity,deformationdensity,spin
density,electrostaticpotential,andmolecularorbitals.
Thisinformation,whenobtainedforseveralgeometriesorisomersorfordifferent
electronicstates,canbeusedtopredictsuchpropertiesasrelativeenergyand
stability,heatofreaction,groundstateelectronconfiguration,electronicabsorption
spectrum,electronicmoments,relativereactivityofdifferentmolecules,andrelative
reactivityofvariousbindingsiteswithinasinglemolecule.

DMolTheInsightandstandalonemodesof
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operation
DMolcanberunasastandaloneprogramorasanapplicationwithintheInsightII
graphicalmolecularmodelinginterface,whichisavailablefromMSIunderseparate
license.
WhenusedwithintheInsightinterface,DMolisaccessibleasoneofitsapplication
modules.(Formoreinformationonthebasicoperations,procedures,and
functionalityoftheInsightprogram,pleaserefertotheInsightdocumentation.)The
functionalityinDMolisaccessedthroughpulldownsthatcontainthecommandsto
setuptheinputcontrolfileforaDMoljob.Theparameterblockforeachcommand
providesyouwithmanyusefuldefaultsandpresetstrategies,allofwhichcanbe
easilymodified,ifnecessary,foryourparticularcalculation.Referencestoatomsor
residuescanbetypedinorcanbespecifiedbypickingtheappropriateatomor
residueinthedisplayedstructure.Youcanthenstarttherunwhileremaininginthe
Insightenvironment.
TheparameterblocksintheInsightinterfacecanalsobeusedtoprepareinputfiles
forrunningDMolinthestandalonemode.Theseinputfilescanbeeditedtodevelop
moresophisticatedcomputationalstrategiesorforrepetitivecalculationsbetter
suitedtotheautomaticcontrolofbatchqueues.
WhenrunasastandaloneprogramoutsidetheInsightenvironment,DMolusesa
simpleuserinterfaceinwhichyoucreateacommandinputfilethatinstructsDMol
whattodo.

ComparisonoftheInsightandstandalone
modesofDMol
RunningDMolintheInsightenvironmentprovidesyouwithadvancedtoolsfor
building,editing,andmanipulating3Dmoleculesandforcreatinginputfilesand
jobscriptsthroughcommandmenus("parameterblocks").However,notallthe
featuresandcapabilitiesofDMolareaccessiblethroughtheInsightinterface.For
thisreason,itcanbeadvantageoustofirstcreateyourmolecule,inputfile,andjob
scriptfilewithintheInsightinterface,thenleavetheInsightenvironmentandedit
thesefilesbyhandorviathestandaloneinterface.
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Whensetupinthestandalonemode,DMolhassomecapabilitiesthatarenot
accessiblethroughtheInsightinterface.Forexample,itallows:
Userdefinedbasis.
Tuningofintegrationmesh.
Userdefinedoccupationnumbers.

StartingDMol
DMolcanbeinvokedwithintheInsightprogrambyselectingDMolfromthe
Modulepulldown(i.e.,theMSIlogo).Severalnewpulldownsappearonthelower
menubar:Setup,Symmetry,Optimize,Environment,Background_Job,Run,
andAnalyze.MostofthecommandsintheseDMolpulldownsareactuallyusedto
setuptheinputfileDMolisnotactuallyrununtiltheRun/Run_DMolcommand
isexecuted.
YoucanalsosetupandrunDMolindependentlyoftheInsightinterface.The
standaloneuserinterfaceisactivatedasdescribedunderDMolinputpreparation
utility:dmol_master.ThisinterfacepromptsyouasyousetuptheDMol
calculation.

Usingthisguide
Thisguidecontainsinstructionsforpreparinginputfiles,runningjobs,and
interpretingoutput.Inaddition,itpresentstheoreticalinformationontheDFT
method.Introduction,TheoryandImplementation,andGeneralMethodology,
References,Glossary.Files,andUtilitiescontainbackgroundinformationthatis
relevanttoboththeInsightandstandalonemodesofusingDMol.
GeneralInformation
TheoryandImplementationpresentsthetheoriesuponwhichthefunctionalitiesof
DMolarebased.ItiswrittenmainlyforthetypicalscientistuserofDMol.This
sectionalsopresentssomeinformationonhowthefunctionalitiesareimplemented.
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GeneralMethodologypresentsthegeneralprocedureforusingDMol,eitherinthe
Insightenvironmentorinthestandalonemode.
Referencescontainsthescientificreferencescitedinthisdocumentation,and
Glossaryincludestermsandsymbols.Thefileformatsaredocumentedhereforthe
filesusedbymorethanoneprogramandunderFilesforfilesspecifictoDMol.
InformationonusingtheDAtomutility,runningbackgroundjobsintheInsight
environment,changingmemoryallocation,andrecompilingDMoliscontainedin
Utilities.
UsingDMolviaInsightinterface
CommandSummaryTheInsightEnvironment,MethodologyInsight,andTutorial
TheInsightEnvironmentcontaininformationthatisspecifictousingDMolinthe
Insightenvironment.CommandSummaryTheInsightEnvironmentbriefly
summarizesthemainfunctionsofeachcommand.MethodologyInsightexplains
howtouseDMolintheInsightmode,whileTutorialTheInsightEnvironment
describesseveraltutoriallessonsthatshowyouhowtouseit.
UsingDMolinstandalonemode
CommandSummaryStandaloneMode,MethodologyStandaloneModeand
CommandsStandaloneModecontaininformationthatisspecifictousingDMolin
thestandalonemode.CommandSummaryStandaloneModebrieflysummarizes
themaincommands,andMethodologyStandaloneModeexplainshowtouse
DMolinthestandalonemode.CommandsStandaloneModeexplainsthe
standalonekeywordsindetail.
InadditiontothemainTableofContentsandIndex,aCrossIndexofOldandNew
Keywordsisincluded.

Additionalinformation
InadditiontothisprintedDMoldocumentation,onlinehelpisavailableand
activatedbyclickingthehelpicon(whichisthebuttoncontainingaquestionmark,
onthesideofthemainInsightwindow)ortheHelppulldown.Printoutscanbe
obtainedthroughthishelputility.
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Helpcanalsobeobtainedduringinputpreparationwiththedmol_masterand
dialoginterfaces,byenteringhelp.
InformationpertainingspecificallytotheInsightinterfaceanditsdefaultmodulesis
containedintheInsightdocumentation.FilesthatarerelevanttoseveralMSI
productsaredocumentedinseparateFileFormatsdocumentation.
Technicalinformationthatismainlyofusetoprogrammersandsystem
administratorsiscontainedintheSystemGuide.TheReleaseNotesinclude
informationonnewfeatures.

Notesoncommandnames
InreferringtocommandsthatareusedwhenrunningDMolinteractivelythrough
theInsightinterface,thisguideusestheformatPulldown/Command,sinceyou
mustusethemousetofirstselectthepulldown,beforethecommandnameappears.
Note,however,thatifyouentercommandsinthecommandareanearthebottomof
theInsightwindow,thecommandnamesmustbeenteredintheformatCommand
PulldownorCommand(whicheverappearsatthetopoftheequivalentparameter
block).
Forconventionsusedindocumentingthestandalonecommands,pleasesee
CommandsStandaloneMode.

LastupdatedSeptember25,1997at03:12PMPDT.
Copyright1997,MolecularSimulations,Inc.Allrightsreserved.

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